Genetic parameters of egg defects and egg quality in layer chickens.

Genetic parameters were estimated for egg defects, egg production, and egg quality traits. Eggs from 11,738 purebred brown-egg laying hens were classified as salable or as having one of the following defects: bloody, broken, calcium deposit, dirty, double yolk, misshapen, pee-wee, shell-less, and soft shelled. Egg quality included albumen height, egg weight, yolk weight, and puncture score.

Improved estimation of the noncentrality parameter distribution from a large number of t-statistics, with applications to false discovery rate estimation in microarray data analysis.

Given a large number of t-statistics, we consider the problem of approximating the distribution of noncentrality parameters (NCPs) by a continuous density. This problem is closely related to the control of false discovery rates (FDR) in massive hypothesis testing applications, e.g.

PPARγ as a therapeutic target in cystic fibrosis.

Cystic fibrosis (CF) is characterized by a proinflammatory pulmonary condition that may result from increased infections and altered intracellular metabolism in CFTR-deficient cells. The lipid-activated transcription factor peroxisome proliferator-activated receptor-γ (PPARγ) has well-established roles in immune cell function and inflammatory modulation and has been demonstrated to play an important role in the heightened inflammatory response in CF cells. Here, we summarize current literature describing PPARγ-dependent alterations of CF cells and discuss the potential of PPARγ ligands for treating CF.

Effects of ad libitum and restricted feeding on early production performance and body composition of Yorkshire pigs selected for reduced residual feed intake.

Residual feed intake (RFI), defined as the difference between observed and expected feed intake based on growth and backfat, has been used to investigate genetic variation in feed efficiency in cattle, poultry and pigs. However, little is known about the biological basis of differences in RFI in pigs. To this end, the objective of this study was to evaluate the fifth generation of a line of pigs selected for reduced RFI against a randomly selected Control line for performance, carcass and chemical carcass composition and overall efficiency.

Optimal use of regression models in genome-wide association studies.

The performance of linear regression models in genome-wide association studies is influenced by how marker information is parameterized in the model. Considering the impact of parameterization is especially important when using information from multiple markers to test for association. Properties of the population, such as linkage disequilibrium (LD) and allele frequencies, will also affect the ability of a model to provide statistical support for an underlying quantitative trait locus (QTL).

Evidence for a major QTL associated with host response to porcine reproductive and respiratory syndrome virus challenge.

Porcine reproductive and respiratory syndrome (PRRS) causes decreased reproductive performance in breeding animals and increased respiratory problems in growing animals, which result in significant economic losses in the swine industry. Vaccination has generally not been effective in the prevention of PRRS, partially because of the rapid mutation rate and evolution of the virus. The objective of the current study was to discover the genetic basis of host resistance or susceptibility to the PRRS virus through a genome-wide association study using data from the PRRS Host Genetics Consortium PRRS-CAP project.

Accuracies of genomic breeding values in American Angus beef cattle using K-means clustering for cross-validation.

Background: Genomic selection is a recently developed technology that is beginning to revolutionize animal breeding. The objective of this study was to estimate marker effects to derive prediction equations for direct genomic values for 16 routinely recorded traits of American Angus beef cattle and quantify corresponding accuracies of prediction.

Methods: Deregressed estimated breeding values were used as observations in a weighted analysis to derive direct genomic values for 3570 sires genotyped using the Illumina BovineSNP50 BeadChip.

Use of bioinformatic SNP predictions in differentially expressed genes to find SNPs associated with Salmonella colonization in swine.

Asymptomatic Salmonella-carrier pigs present a major problem in preharvest food safety, with a recent survey indicating >50% of swine herds in the United States have Salmonella-positive animals. Salmonella-carrier pigs serve as a reservoir for contamination of neighbouring pigs, abattoir pens and pork products. In addition, fresh produce as well as water can be contaminated with Salmonella from manure used as fertilizer.

Integrating comparative expression profiling data and association of SNPs with Salmonella shedding for improved food safety and porcine disease resistance.

Salmonella in swine is a major food safety problem, as the majority of US swine herds are Salmonella-positive. Salmonella can be shed from colonized swine and contaminate (i) neighbouring pigs; (ii) slaughter plants and pork products; (iii) edible crops when swine manure is used as a fertilizer; and (iv) water supplies if manure used as crop fertilizer runs off into streams and waterways. A potentially powerful method of addressing pre-harvest food safety at the farm level is through genetic improvement of disease resistance in animals.

Bayesian analysis of the effect of selection for residual feed intake on growth and feed intake curves in Yorkshire swine.

Gompertz growth functions were fitted to longitudinal measurements of daily feed intake (DFI) and BW of 586 boars and 495 gilts from a selection experiment in Yorkshire pigs for residual feed intake (RFI). The selection experiment consists of a line selected for low residual feed intake (LRFI) for 5 generations and a randomly selected control line (CTRL). The objectives of this study were to use Bayesian methods to estimate genetic parameters of the Gompertz curve parameters for DFI and BW, to evaluate the effect of selection for reduced RFI on the Gompertz parameters and shape of curves for DFI and BW, and to develop methodology for quantifying genetic variation at the level of the original phenotypes for DFI and BW based on the Bayesian analysis of the nonlinear model.

Mapping genetic loci that interact with myostatin to affect growth traits.

Myostatin, or GDF8, is an inhibitor of skeletal muscle growth. A non-functional myostatin mutation leads to a double muscling phenotype in some species, for example, mice, cattle and humans. Previous studies have indicated that there are loci in the genome that interact with myostatin to control backfat depth and other complex traits.

Effectiveness of phone and e-mail lifestyle counseling for long term weight control among overweight employees.

Objectives: To determine the effectiveness of a weight-management program with personal counseling by phone or e-mail.

Methods: A randomized controlled trial of a 6-month program comparing two modes of intervention delivery (phone, n = 462; Internet, n = 464) with self-directed materials (control, n = 460), among overweight employees. Change in body weight after 2 years was the main outcome.

Genomic breeding value prediction and QTL mapping of QTLMAS2010 data using Bayesian Methods.

Background: Bayesian methods allow prediction of genomic breeding values (GEBVs) using high-density single nucleotide polymorphisms (SNPs) covering the whole genome with effective shrinkage of SNP effects using appropriate priors. In this study we applied a modification of the well-known BayesA and BayesB methods to estimate the proportion of SNPs with zero effects (π) and a common variance for non-zero effects. The method, termed BayesCπ, was used to predict the GEBVs of the last generation of the QTLMAS2010 data.

Genetic analysis of longitudinal measurements of performance traits in selection lines for residual feed intake in Yorkshire swine.

A 5-generation selection experiment in Yorkshire pigs for feed efficiency consists of a line selected for low residual feed intake (LRFI) and a random control line (CTRL). The objectives of this study were to use random regression models to estimate genetic parameters for daily feed intake (DFI), BW, backfat (BF), and loin muscle area (LMA) along the growth trajectory and to evaluate the effect of LRFI selection on genetic curves for DFI and BW. An additional objective was to compare random regression models using polynomials (RRP) and spline functions (RRS).

Comparative effectiveness of lifestyle interventions on cardiovascular risk factors among a Dutch overweight working population: a randomized controlled trial.

Background: Overweight (Body Mass Index [BMI] ≥ 25 kg/m²) and obesity (BMI ≥ 30 kg/m²) are associated with increased cardiovascular risk, posing a considerable burden to public health. The main aim of this study was to investigate lifestyle intervention effects on cardiovascular risk factors in healthy overweight employees.

Methods: Participants were 276 healthy overweight employees (69.

Breeding value prediction for production traits in layer chickens using pedigree or genomic relationships in a reduced animal model.

Background: Genomic selection involves breeding value estimation of selection candidates based on high-density SNP genotypes. To quantify the potential benefit of genomic selection, accuracies of estimated breeding values (EBV) obtained with different methods using pedigree or high-density SNP genotypes were evaluated and compared in a commercial layer chicken breeding line.

Methods: The following traits were analyzed: egg production, egg weight, egg color, shell strength, age at sexual maturity, body weight, albumen height, and yolk weight.

Evaluation of egg production in layers using random regression models.

The objectives of this study were to estimate genetic parameters for egg production over the age trajectory in 3 layer lines, which represent different biotypes for egg production, and to validate the use of breeding values for slope as a measure of persistency to be used in the selection program. Egg production of more than 26,000 layers per line from 6 consecutive generations were analyzed with a random regression model with a within-hatch-nested fifth-order fixed-regression polynomial and linear polynomials for random additive genetic and permanent environmental effects. Daily records were cumulated into biweekly periods.

Effect of selection for residual feed intake on feeding behavior and daily feed intake patterns in Yorkshire swine.

Residual feed intake (RFI) is a measure of feed efficiency defined as the difference between observed and predicted feed intake based on average requirements for growth and maintenance. The objective of this study was to evaluate the effect of selection for decreased RFI on feeding behavior traits and to estimate their relationships with RFI. Three data sets from the 4th and 5th generations of a selection experiment with a line selected for reduced RFI (LRFI) and a randomly selected control line (CTRL) were analyzed.

Variability of fatigue during the day in patients with primary Sjögren's syndrome, systemic lupus erythematosus, and rheumatoid arthritis.

Objectives: Fatigue is a common complaint of patients with primary Sjögren's syndrome (pSS), systemic lupus erythematosus (SLE), and rheumatoid arthritis (RA). The aim of this study was to examine and compare in patients with these diseases the course of fatigue within the first hour after awakening and during the day, and to examine sleep disturbance as a potential determinant of fatigue.

Methods: Eight repeated measurements at 5 fatigue dimensions were assessed on 2 consecutive days in the natural environment of female patients with pSS (n=29), SLE (n=23), RA (n=19), and healthy women (n=52).

Effects of ad libitum and restricted feed intake on growth performance and body composition of Yorkshire pigs selected for reduced residual feed intake.

Residual feed intake (RFI), defined as the difference in the observed and expected feed intake while accounting for growth and backfat, has gained much attention, but little is known about why pigs selected for reduced RFI are more efficient. To this end, a line of Yorkshire pigs selected for reduced RFI was developed. The objective of this study was to evaluate the 5th generation of this select line against a randomly selected control line for performance, carcass and chemical carcass composition, and overall efficiency toward the later part of the growth phase.

The effect of selection for residual feed intake on general behavioral activity and the occurrence of lesions in Yorkshire gilts.

The objectives of this study were to determine the effect of selection for improved residual feed intake on behavior, activity, and lesion scores in gilts in their home pen. A total of 192 gilts were used, 96 from a line that had been selected for decreased residual feed intake over 5 generations (LRFI) and 96 from a randomly bred control line. Gilts were housed in 12 pens (16 gilts/pen; 0.

Effects of selection for decreased residual feed intake on composition and quality of fresh pork.

The objectives of this study were to determine the extent to which selection for decreased residual feed intake (RFI) affects pork composition and quality. Pigs from the fifth generation of selection for decreased RFI (select) and a randomly selected line (control) were utilized. Two experiments were conducted.

A gene frequency model for QTL mapping using Bayesian inference.

Background: Information for mapping of quantitative trait loci (QTL) comes from two sources: linkage disequilibrium (non-random association of allele states) and cosegregation (non-random association of allele origin). Information from LD can be captured by modeling conditional means and variances at the QTL given marker information. Similarly, information from cosegregation can be captured by modeling conditional covariances.

Predicting allele frequencies in DNA pools using high density SNP genotyping data.

To evaluate the ability to use DNA pools with the Illumina Infinium genotyping platform, two sets of gradient pools were created using two pairs of highly inbred chicken lines. Replicate pools containing 0%, 10%, 20%, 40%, 60%, 80%, 90% and 100% of DNA from line A vs. B or line C vs.